This is the second paper of the series aimed at understanding the ensemble of instanton-dyons, now with two flavors of light dynamical quarks. The partition function is appended by the fermionic factor, $(det T)^{N_f}$ and Dirac eigenvalue spectra at small values are derived from the numerical simulation of 64 and 128 dyons. Those spectra show clear chiral symmetry breaking pattern at high dyon density.